Amid a crisis in affordable housing, the city’s Housing Authority kept 80 low-rent apartments empty for more than 10 years for repairs and renovations — including one dating back to 1994, Comptroller Scott Stringer found in an audit.

Apartments in need of repair were taken off-line for an average of seven years, and even transferring a working unit from one tenant to another took the agency 116 days on average, the review found.

Overall, the audit found 2,342 units vacant — out of a total 178,000 apartments overseen by the Housing Authority — as of September 2014.

“It’s beyond the realm of explanation how years can pass before apartments become habitable,” Stringer said Wednesday.

“The more than 270,000 New Yorkers who are waiting for housing deserve much better treatment than that.”

Stringer said the vacancies for repair work alone cost the authority at least $7.7 million in lost rent.

His auditors also dinged the Housing Authority for not keeping proper watch over empty apartments, noting that a handful showed signs of recent visits by squatters.

But agency officials shot back that no money had been lost for unrented apartments under federal reimbursement rules and that the vacancy rate has been reduced by nearly 40 percent over the past two years.

The agency said repair delays are largely driven by a lack of resources, which lead occupied apartments to take precedence over empty ones.

“NYCHA has a record low vacancy rate of only 1 percent—the lowest it’s been in nearly 10 years,” a spokeswoman said.

Authority officials said many of the long-term vacancies stem from leaks in apartments that can’t be abated without complete roof replacements.

They said they hope that problem will be alleviated after a recent infusion of $300 million in capital funds for roof repairs from the city.